i own the SAM440ep(mini) and my onboard M9 died some month ago. So i put an Radeon9250 on the PCI-Slot. Sadly the Slot is only 33Mhz and DMA don't work, that makes it terrible slow in compare with the 66Mhz DMA onboard M9.

Because of Science and Support, i bought the HD-Driver to Support this great Project.

I test a HD2400XT that i found in our Companys Electro-Recycle-Bin. The Adaptor is this PEX8112 thing.

* on some Sam440ep boards, the MMUCR register is not set correctly at bootstrap.
This leads to poor write L1 cache performances.
The utility check the register, and if needed, modify it.

* on all Sam440ep boards with a Radeon card enables read prefetching for graphic ram.
If a Radeon card is detected, the utility will modify the POM2 PCI registers to
enable read prefetching.
This speed up reads for the gfx card from 15 MB/s to 30 MB/s on a M9 card.

* set the Latency Timer on the 440ep PCI Bridge,
With this new setting read speed increase around 50% on Radeon PCI cards
(up to 42 MB/s on a M9 card) and around 200% on RadeonHD PCI cards

Here are the results for the Memcopy part of the GfxBench2D that I did a few weekes ago on my Sam440ep-Flex 800Mhz .Using the second slot # 33mHz and the first slot # 66MHz. Note the write pixel array score is almost 10 times faster with DMA and a 66mhz slot.I have the Sam440ep_setup utility enabled.This is with a Radeon HD5670 and adapter .

try activating the tooltype SNDGFX in the Sam440ep_Setup utility by removing the brackets.
The Graphics card in the PCI slot is the secondary card in your case.In the default setting the speed up is being applied for your onboard M9.